BLiSS REPORT (2013-14) - Establishment of Biotech Labs in Senior Secondary Schools (BLiSS) in North Eastern States of India
27th Co-ordinators meeting to be held in Nainital from 3-5 March, 2016
National Symposium on Bioinformatics was held at University of Jammu on February 2, 2012
Compendium on Bioinformatics publications released during 23rd Co-ordinators meeting
 
   
R & D PROJECTS
 
  R&D IN BIOINFORMATICS  
  The department has received many conceptualized project proposals for carrying out research in the field of Bioinformatics and Computational Biology. It has been witnessed that the generation of primary data have increased in the country with the support of several Government departments like DBT. During this year, the department has supported 10 R&D projects which are specific to applications in the area of Agriculture, Medical and Knowledge Discovery from Data (KDD) by using Bioinformatics tools. The R&D projects which were supported earlier have also shown very good progress. The projects which had shown major outcomes in terms of scientific utility and product development are highlighted below.

(i) Mango Database

Through a project supported to the Central Institute of Sub-Tropical Horticulture, Lucknow on Development of Genetic resource database and information system for mango, a database front-end has been developed using MySQL and PHP dealing with updating and retrieval of data. Data on morphological and molecular characterization was collected from NAGS and database on the mango accessions in different genebanks has been developed. The characterization data of 200 accessions was converted into codes and used for updating of the data. Information on various aspects of Mangifera was collected and is been converted into digital format for adding it to the database. A website on Mango Genetic Resource Information System has been developed and is being tested for security options, so that it is enriched by uploading collected information as database with protection against unauthorized access.

(ii) Interactive Visual Diagnostic software to Check Nutrient Deficiency in Crops

An interactive Visual Diagnostic Software for the Identification of Nutrient Deficiencies in Crops is being implemented at TNAU, Coimbatore. A software has been developed based on the concept that plants are the indicator of nutrient deficiencies in soils that commensurate with a proverb “Face is the Index of the Mind”. The nutrient deficiencies exhibited by plants are very unique and distinguishable from one another depending on the mobility of ions and the physiological functions associated with it. To accomplish the task four approaches namely (a) identification of nutrient deficiencies using visual symptoms in the field, (b) classification based on dichotomous keys, (c) confirmation through soil and plant analyses and (d) scanning and integration of the images into the visual basic software.

Nutrient deficiency symptoms occurring in a wide array of crops (about 65) in seven agro-climatic zones of Tamil Nadu had been photographed using a high resolution digital camera. In the same location, soil and plant samples have been collected and analysed for its nutrient concentrations in order to relate whether symptoms associated with a particular nutrient deficiency. In maize, sugarcane, sorghum, soybean and groundnut, visual deficiency symptoms were graded and analyzed for their specific Fe and P concentrations. These experiments have reconfirmed that visual diagnosis closely coincides with the deficiency in soils vis-a-vis in plants. After confirmation, the photographic images were compressed by optimization process to reduce the file size to fit into the Visual Basic Software. The Visual Diagnostic Software has been developed and about 70% symptoms taken from the field had been integrated. Besides the software, a book on 'Diagnosis of Nutrient Deficiencies in Crops' in English and Tamil has been prepared to be able to provide basic information for the user groups.

(iii) Myocilin Structure Prediction using Knowledge based consensus.

A project on Understanding Protein Aggregation in relation to Primary Open Angle Glaucoma (POAG) for evaluating models, Screening Polymorphisms and database development is being pursued jointly by MKU, Madurai and Aravind Eye Hospital Madurai. Mutations in Human Myocilin, a 55-kDa protein has been associated with open angle glaucoma. Most of these mutations are segregated to the olfactomedin-like domain. Only 2-4% of POAG patients have mutations in the myocilin gene. Understanding the structure and folding of the native protein and the mutants that increase aggregation could lead to possible prevention of the condition.

A plausible structure predicted for myocilin using a knowledge based consensus method was used to understand the role of myocilin and these mutations in POAG. The model resulted in a beta strand rich C-term Region (181 – 504) having the Cys245-Cys433 disulfide bone. Molecular dynamics is used to understand the role of the mutations in causing aggregation. For example, Gly367Arg a novel mutation has been identified in the patients from local population. From experimental analysis it has been shown that it aggregates in the trabecular meshwork and is not secreted out, whereas the normal protein is secreted out. Structural analysis and molecular dynamics calculations indicate how the mutation might cause possible conformational change leading to aggregation. A total of 124 genomic variations were screened and six polymorphisms that lead to altered protein products were detected as possible candidates for alternative splicing mechanism.

(iv) Flagship Consortium Projects on TB & Rice Bioinformatics

Two important flagship multi-agency and multi-institutional programs namely Development of Databases on TB & Rice have been conceptualized. Many well known institutions, say about 20 and scientists working in these areas are being associated with these projects for data sources and continuous evaluation at various stages of its implementations.

 
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